Molecular motors, such as myosin, have evolved to transduce chemical energy from ATP into mechanical work to drive essential cellular processes, from muscle contraction to vesicular transport. Dysfunction in these motors is a root cause of many pathologies necessitating the application of intrinsic control over molecular motor function. We hypothesized that altering the myosin’s energy substrate via minor positional changes to the triphosphate portion of the molecule will allow us to control the protein and affect its in vitro function. We utilized positional isomers of a synthetic non-nucleoside triphosphate, azobenzene triphosphate, and assessed whether myosin’s force- and motion-generating capacity could be controlled at both the ensemble and single-molecule levels. This successfully demonstrated the ability to alter a substrate to exert intrinsic control over a protein’s function by affecting distinct steps in myosin’s chemomechanical cycle. A deeper investigation of the mechanisms underlying any enhancement or inhibition of myosin’s function may reveal potential avenues for novel approaches to treat certain myopathies.